[2023-03-16 05:41:22,605] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:41:22,606] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:41:22,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference
[2023-03-16 05:41:23,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:41:23,713] [INFO] Task started: Prodigal
[2023-03-16 05:41:23,713] [INFO] Running command: cat /var/lib/cwl/stg446982d5-3bd7-48a1-909e-aff913a7308e/OceanDNA-b42373.fa | prodigal -d OceanDNA-b42373/cds.fna -a OceanDNA-b42373/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:41:28,055] [INFO] Task succeeded: Prodigal
[2023-03-16 05:41:28,055] [INFO] Task started: HMMsearch
[2023-03-16 05:41:28,055] [INFO] Running command: hmmsearch --tblout OceanDNA-b42373/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/reference_markers.hmm OceanDNA-b42373/protein.faa > /dev/null
[2023-03-16 05:41:28,194] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:41:28,195] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg446982d5-3bd7-48a1-909e-aff913a7308e/OceanDNA-b42373.fa]
[2023-03-16 05:41:28,203] [INFO] Query marker FASTA was written to OceanDNA-b42373/markers.fasta
[2023-03-16 05:41:28,203] [INFO] Task started: Blastn
[2023-03-16 05:41:28,203] [INFO] Running command: blastn -query OceanDNA-b42373/markers.fasta -db /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/reference_markers.fasta -out OceanDNA-b42373/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:28,634] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:28,634] [INFO] Selected 10 target genomes.
[2023-03-16 05:41:28,634] [INFO] Target genome list was writen to OceanDNA-b42373/target_genomes.txt
[2023-03-16 05:41:28,639] [INFO] Task started: fastANI
[2023-03-16 05:41:28,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg446982d5-3bd7-48a1-909e-aff913a7308e/OceanDNA-b42373.fa --refList OceanDNA-b42373/target_genomes.txt --output OceanDNA-b42373/fastani_result.tsv --threads 1
[2023-03-16 05:41:32,298] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:32,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:41:32,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:41:32,299] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:41:32,299] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:41:32,299] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-16 05:41:32,299] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42373/tc_result.tsv
[2023-03-16 05:41:32,299] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:41:32,299] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:41:32,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/checkm_data
[2023-03-16 05:41:32,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:41:32,305] [INFO] Task started: CheckM
[2023-03-16 05:41:32,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42373/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42373/checkm_input OceanDNA-b42373/checkm_result
[2023-03-16 05:41:49,002] [INFO] Task succeeded: CheckM
[2023-03-16 05:41:49,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:41:49,004] [INFO] ===== Completeness check finished =====
[2023-03-16 05:41:49,004] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:41:49,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42373/markers.fasta)
[2023-03-16 05:41:49,005] [INFO] Task started: Blastn
[2023-03-16 05:41:49,005] [INFO] Running command: blastn -query OceanDNA-b42373/markers.fasta -db /var/lib/cwl/stg85e4eb2a-4734-4081-8823-2b32a943c432/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42373/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:49,426] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:49,427] [INFO] Selected 14 target genomes.
[2023-03-16 05:41:49,427] [INFO] Target genome list was writen to OceanDNA-b42373/target_genomes_gtdb.txt
[2023-03-16 05:41:49,442] [INFO] Task started: fastANI
[2023-03-16 05:41:49,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg446982d5-3bd7-48a1-909e-aff913a7308e/OceanDNA-b42373.fa --refList OceanDNA-b42373/target_genomes_gtdb.txt --output OceanDNA-b42373/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:41:52,328] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:52,334] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:41:52,335] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	99.4789	277	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	81.4217	222	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607365.1	s__SCGC-AAA076-P13 sp018607365	81.0103	224	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	77.9387	118	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	77.7606	88	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.7405	83	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	77.7284	111	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902515155.1	s__SCGC-AAA076-P13 sp902515155	77.4362	93	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	77.3882	100	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902617045.1	s__SAR86A sp902617045	76.8491	67	292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-16 05:41:52,335] [INFO] GTDB search result was written to OceanDNA-b42373/result_gtdb.tsv
[2023-03-16 05:41:52,335] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:41:52,336] [INFO] DFAST_QC result json was written to OceanDNA-b42373/dqc_result.json
[2023-03-16 05:41:52,336] [INFO] DFAST_QC completed!
[2023-03-16 05:41:52,336] [INFO] Total running time: 0h0m30s